18-23305164-C-T

Position:

• chr18-23305164-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032933.6(TMEM241):​c.830+4516G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,074 control chromosomes in the GnomAD database, including 20,870 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.52 (20870 hom., cov: 33)
• Consequence: TMEM241 NM_032933.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

Genes affected

TMEM241 (HGNC:31723): (transmembrane protein 241) Predicted to enable antiporter activity. Predicted to be involved in carbohydrate transport and transmembrane transport. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

TMEM241 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM241	NM_032933.6	c.830+4516G>A		intron_variant		ENST00000383233.8	NP_116322.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM241	ENST00000383233.8	c.830+4516G>A		intron_variant		1	NM_032933.6	ENSP00000372720.3

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79045 AN: 151956 Hom.: 20856 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.535

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.520 AC: 79103 AN: 152074 Hom.: 20870 Cov.: 33 AF XY: 0.521 AC XY: 38689 AN XY: 74330

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.531

Alfa AF: 0.555 Hom.: 29964

Bravo AF: 0.505

Asia WGS AF: 0.533 AC: 1854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	4.2
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12326518; hg19: chr18-20885128;